Katriona Shea's research while affiliated with Pennsylvania State University and other places
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Publications (223)
Our ability to forecast epidemics far into the future is constrained by the many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify the future state of critical epidemic drivers. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multipl...
Importance: COVID-19 continues to cause significant hospitalizations and deaths in the United States. Its continued burden and the impact of annually reformulated vaccines remain unclear.
Objective: To project COVID-19 hospitalizations and deaths from April 2023–April 2025 under two plausible assumptions about immune escape (20% per year and 50% pe...
Anthropogenic activities expose many ecosystems to multiple novel disturbances simultaneously. Despite this, how biodiversity responds to simultaneous disturbances remains unclear, with conflicting empirical results on their interactive effects. Here, we experimentally test how one disturbance (an invasive species) affects the diversity of a commun...
Across many fields, scenario modeling has become an important tool for exploring long-term projections and how they might depend on potential interventions and critical uncertainties, with relevance to both decision makers and scientists. In the past decade, and especially during the COVID-19 pandemic, the field of epidemiology has seen substantial...
A central question in biodiversity conservation is whether species will maintain viable population dynamics under future climate change. Assessing species extinction risk under climate warming requires demographic studies integrating vital rate responses to long-term warming throughout species’ life cycle. However, studies of this nature are rare....
Our ability to forecast epidemics more than a few weeks into the future is constrained by the complexity of disease systems, our limited ability to measure the current state of an epidemic, and uncertainties in how human action will affect transmission. Realistic longer-term projections (spanning more than a few weeks) may, however, be possible und...
Policymakers must make management decisions despite incomplete knowledge and conflicting model projections. Little guidance exists for the rapid, representative, and unbiased collection of policy-relevant scientific input from independent modeling teams. Integrating approaches from decision analysis, expert judgment, and model aggregation, we conve...
Managing social‐ecological systems (SES) requires balancing the need to tailor actions to local heterogeneity and the need to work over large areas to accommodate the extent of SES. This balance is particularly challenging for policy since the level of government where the policy is being developed determines the extent and resolution of action.
We...
The COVID-19 Vaccines Global Access (COVAX) is a World Health Organization (WHO) initiative that aims for an equitable access of COVID-19 vaccines. Despite potential heterogeneous infection levels across a country, countries receiving allotments of vaccines may follow WHO’s allocation guidelines and distribute vaccines based on a jurisdictions’ rel...
Probabilistic predictions support public health planning and decision making, especially in infectious disease emergencies. Aggregating outputs from multiple models yields more robust predictions of outcomes and associated uncertainty. While the selection of an aggregation method can be guided by retrospective performance evaluations, this is not a...
Background
The COVID-19 Scenario Modeling Hub convened nine modeling teams to project the impact of expanding SARS-CoV-2 vaccination to children aged 5–11 years on COVID-19 burden and resilience against variant strains.
Methods
Teams contributed state- and national-level weekly projections of cases, hospitalizations, and deaths in the United State...
Climate change is bringing unforeseen alterations to disturbance regimes, exposing many ecosystems to multiple novel disturbances simultaneously. Despite this, how biodiversity responds to simultaneous disturbances remains unclear, with conflicting empirical results on their interactive effects. Here, we experimentally test how one disturbance (an...
The structure of contact networks affects the likelihood of disease spread at the population scale and the risk of infection at any given node. Though this has been well characterized for both theoretical and empirical networks for the spread of epidemics on completely susceptible networks, the long-term impact of network structure on risk of infec...
Mathematical modelling is used during disease outbreaks to compare control interventions. Using multiple models, the best method to combine model recommendations is unclear. Existing methods weight model projections, then rank control interventions using the combined projections, presuming model outputs are directly comparable. However, the way eac...
In Spring 2021, the highly transmissible SARS-CoV-2 Delta variant began to cause increases in cases, hospitalizations, and deaths in parts of the United States. At the time, with slowed vaccination uptake, this novel variant was expected to increase the risk of pandemic resurgence in the US in summer and fall 2021. As part of the COVID-10 Scenario...
![Fig 1. The community assembly model of Campbell et al. [72]....](publication/361161565/figure/fig1/AS:1165127793545218@1654799521734/The-community-assembly-model-of-Campbell-et-al-72-Interactions-between-plants_Q320.jpg)
The impact of invasion by a single non-native species on the function and structure of ecological communities can be significant, and the effects can become more drastic–and harder to predict–when multiple species invade as a group. Here we modify a dynamic Boolean model of plant-pollinator community assembly to consider the invasion of native comm...
Disturbances are important determinants of diversity, and the combination of their aspects (e.g., disturbance intensity, frequency) can result in complex diversity patterns. Here, we leverage an important approach to classifying disturbances in terms of temporal span to understand the implications for species coexistence: pulse disturbances are acu...
Climate change alters many aspects of weed performance, and may also alter the effectiveness of management practices to control pests. Despite this concern, entire categories of widely‐used management practices, such as physical control, remain understudied in this context. We conducted a field experiment growing the invasive pest musk thistle (Car...
Disturbances can facilitate biological invasions, with the associated increase in resource availability being a proposed cause. Here, we experimentally tested the interactive effects of disturbance regime (different frequencies of biomass removal at equal intensities) and resource abundance on invasion success using a factorial design containing fi...
Dispersal drives invasion dynamics of non‐native species and pathogens. Applying knowledge of dispersal to optimize management of invasions can mean the difference between a failed or successful control program and dramatically improve return on investment of control efforts. A common approach for identifying optimal management solutions for invasi...
Background
SARS-CoV-2 vaccination of persons aged 12 years and older has reduced disease burden in the United States. The COVID-19 Scenario Modeling Hub convened multiple modeling teams in September 2021 to project the impact of expanding vaccine administration to children 5-11 years old on anticipated COVID-19 burden and resilience against variant...
The estimation of parameters and model structure for informing infectious disease response has become a focal point of the recent pandemic. However, it has also highlighted a plethora of challenges remaining in the fast and robust extraction of information using data and models to help inform policy. In this paper, we identify and discuss four broa...
Stay-at-home orders and shutdowns of non-essential businesses are powerful, but socially costly, tools to control the pandemic spread of SARS-CoV-2. Mass testing strategies, which rely on widely administered frequent and rapid diagnostics to identify and isolate infected individuals, could be a potentially less disruptive management strategy, parti...
Background
The development of public health policy is inextricably linked with governance structure. In our increasingly globalized world, human migration and infectious diseases often span multiple administrative jurisdictions that might have different systems of government and divergent management objectives. However, few studies have considered...
What is already known about this topic?
The highly transmissible SARS-CoV-2 Delta variant has begun to cause increases in cases, hospitalizations, and deaths in parts of the United States. With slowed vaccination uptake, this novel variant is expected to increase the risk of pandemic resurgence in the US in July-December 2021.
What is added by this...
The structure of contact networks affects the likelihood of disease spread at the population scale and the risk of infection at any given node. Though this has been well characterized for both theoretical and empirical networks for the spread of epidemics on completely susceptible networks, the long-term impact of network structure on risk of infec...
Stress comprises three sequential stages: the event (stressor), which leads to an initial effect on a focal organism (stress), followed by the organism's ultimate response (recovery or not). Using this framework, we test how the duration and timing of a stressor individually and interactively affect the initial and asymptotic organism outcomes. We...
More than 1.6 million Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) tests were administered daily in the United States at the peak of the epidemic, with a significant focus on individual treatment. Here, we show that objective-driven, strategic sampling designs and analyses can maximize information gain at the population level, which...
After a period of rapidly declining U.S. COVID-19 incidence during January-March 2021, increases occurred in several jurisdictions (1,2) despite the rapid rollout of a large-scale vaccination program. This increase coincided with the spread of more transmissible variants of SARS-CoV-2, the virus that causes COVID-19, including B.1.1.7 (1,3) and rel...
The management of biological invasions is a worldwide conservation priority. Unfortunately, decision‐making on optimal invasion management can be impeded by lack of information about the biological processes that determine invader success (i.e. biological uncertainty) or by uncertainty about the effectiveness of candidate interventions (i.e. operat...
Livestock diseases have devastating consequences economically, socially and politically across the globe. In certain systems, pathogens remain viable after host death, which enables residual transmissions from infected carcasses. Rapid culling and carcass disposal are well-established strategies for stamping out an outbreak and limiting its impact;...
A Correction to this paper has been published: https://doi.org/10.1038/s41592-021-01079-6.
During a disease outbreak, healthcare workers (HCWs) are essential to treat infected individuals. However, these HCWs are themselves susceptible to contracting the disease. As more HCWs get infected, fewer are available to provide care for others, and the overall quality of care available to infected individuals declines. This depletion of HCWs may...
Disturbance is a key factor shaping ecological communities, but little is understood about how the effects of disturbance processes accumulate over time. When disturbance regimes change, historical processes may influence future community structure, for example, by altering invasibility compared to communities with stable regimes. Here, we use an a...
The authority to manage natural capital often follows political boundaries rather than ecological. This mismatch can lead to unsustainable outcomes, as spillovers from one management area to the next may create adverse incentives for local decision making, even within a single country. At the same time, one‐size‐fits‐all approaches of federal (cent...
Policymakers make decisions about COVID-19 management in the face of considerable uncertainty. We convened multiple modeling teams to evaluate reopening strategies for a mid-sized county in the United States, in a novel process designed to fully express scientific uncertainty while reducing linguistic uncertainty and cognitive biases. For the scena...
Numerous studies have documented changes in the seasonal timing of organisms’ growth and reproduction in response to climate warming. These changes correlate with documented changes in species’ abundance, but mechanisms linking these trends remain elusive. We investigated the joint demographic effects of advanced reproductive phenology and warming...
During a disease outbreak, healthcare workers (HCWs) are essential to treat infected individuals. However, these HCWs are themselves susceptible to contracting the disease. As more HCWs get infected, fewer are available to provide care for others, and the overall quality of care available to infected individuals declines. This depletion of HCWs may...
“I have no idea what’s awaiting me, or what will happen when this all ends. For the moment I know this: there are sick people and they need curing.” ―Albert Camus, The Plague
Infectious disease epidemics present a difficult task for policymakers, requiring the implementation of control strategies under significant time constraints and uncertainty. Mathematical models can be used to predict the outcome of control interventions, providing useful information to policymakers in the event of such an epidemic. However, these...
Realistic models of epidemics account for latency, loss of immunity, births and deaths.
Musk thistle, Carduus nutans, is a major noxious weed throughout its non-native range. The flower head weevil, Rhinocyllus conicus, deemed likely to be a strong candidate for biocontrol based on laboratory tests, has proven variable in its efficacy, suggesting a possible influence of ecological context. To improve our understanding of the dynamics...
The coronavirus disease 2019 (COVID-19) pandemic has triggered efforts by multiple modeling groups to forecast disease trajectory, assess interventions, and improve understanding of the pathogen. Such models can often differ substantially in their projections and recommendations, reflecting different policy assumptions and objectives, as well as sc...
“Every day sadder and sadder news of its increase. In the City died this week 7496; and of them, 6102 of the plague. But it is feared that the true number of the dead this week is near 10,000 ....” —Samuel Pepys, 1665
Disturbances can play a major role in biological invasions: by destroying biomass, they alter habitat and resource abundances. Previous field studies suggest that disturbance-mediated invader success is a consequence of resource influxes, but the importance of other potential covarying causes, notably the opening up of habitats, have yet to be dire...
Climate warming is likely to change the ways in which plants interact with their insect mutualists, for example through changes in phytochemistry. In particular, this may have implications for the ways in which we manage noxious weeds, which may spread more quickly if they experience stronger mutualistic interactions. We grew the invasive nodding t...
Invasive species that form mutualistic interactions can perturb resident communities by creating new interactions, or weakening the strength of existing interactions via competition. We hypothesized that introducing a super-generalist plant species to bee-plant networks would lead to (1) increases in the weighted and unweighted average degree, nest...
There is growing realization that intraspecific variation in seed dispersal can have important ecological and evolutionary consequences. However, we do not have a good understanding of the drivers or causes of intraspecific variation in dispersal, how strong an effect these drivers have, and how widespread they are across dispersal modes. As a firs...
The distribution and abundance of plants across the world depends in part on their ability to move, which is commonly characterized by a dispersal kernel. For seeds, the total dispersal kernel (TDK) describes the combined influence of all primary, secondary, and higher-order dispersal vectors on the overall dispersal kernel for a plant individual,...
Although dispersal is generally viewed as a crucial determinant for the fitness of any organism, our understanding of its role in the persistence and spread of plant populations remains incomplete. Generalizing and predicting dispersal processes are challenging due to context dependence of seed dispersal, environmental heterogeneity, and interdepen...
Many invasive species managers state that their objective is to “control” an invader. However, the appropriate choice of a management option requires a more explicit statement of management objectives, in terms of both the relevant time horizon and spatial scale. Using data from a 2-yr mowing experiment, we show that the most effective management s...
Non-native plant species reliant on insect pollination must attract novel pollinators in their introduced habitat to reproduce. Indeed, pollination services provided by resident floral visitors may contribute to the spread of non-native species, which may then affect the pollination services received by native plants. To determine the mechanisms by...
Determining how best to manage an infectious disease outbreak may be hindered by both epidemiological uncertainty (i.e. about epidemiological processes) and operational uncertainty (i.e. about the effectiveness of candidate interventions). However, these two uncertainties are rarely addressed concurrently in epidemic studies. We present an approach...
The number of all possible epidemics of a given infectious disease that could occur on a given landscape is large for systems of real-world complexity. Furthermore, there is no guarantee that the control actions that are optimal, on average, over all possible epidemics are also best for each possible epidemic. Reinforcement learning (RL) and Monte...
When climatic or environmental conditions change, plant populations must either adapt to these new conditions, or track their niche via seed dispersal. Adaptation of plants to different abiotic environments has mostly been discussed with respect to physiological and demographic parameters that allow local persistence. However, rapid modifications i...
When climatic or environmental conditions change, plant populations must either adapt to these new conditions, or track their niche via seed dispersal. Adaptation of plants to different abiotic environments has mostly been discussed with respect to physiological and demographic parameters that allow local persistence. However, rapid modifications i...
Seed dispersal enables plants to reach hospitable germination sites and escape natural enemies. Understanding when and how much seed dispersal matters to plant fitness is critical for understanding plant population and community dynamics. At the same time, the complexity of factors that determine if a seed will be successfully dispersed and subsequ...
We present an investigation of the effects of disturbance and fecundity–tolerance strategies on community composition. We develop a theoretical model and apply it to macrofaunal communities at deep‐sea hydrothermal vents. We characterize community outcomes and find that dominance, coexistence, and alternative stable equilibria can all result from t...
Propagule pressure is often considered the most consistent predictor of the success of founding populations. This relationship could be mediated by the composition of the founding group (e.g. level of prior adaptation to the recipient environment or its diversity) as well as the introduction scenario (i.e. the frequency, size and timing of discrete...
In the event of a new infectious disease outbreak, mathematical and simulation models are commonly used to inform policy by evaluating which control strategies will minimize the impact of the epidemic. In the early stages of such outbreaks, substantial parameter uncertainty may limit the ability of models to provide accurate predictions, and policy...
Number of confirmed cases per week (ending Tuesday) during the 2010 outbreak in Miyazaki.
(TIF)
Number of confirmed cases per week (ending Monday) during the 2001 outbreak in the UK.
(TIF)
Predicted final total culls for weeks 1–11 for several control strategies for the 2010 outbreak of foot-and-mouth disease in Miyazaki, Japan.
A) Predictions of final total culls at the first 11 weeks throughout the 2001 outbreak in UK under seven control strategies (week 1 represents 27 April 2010). Columns denoted ‘Ac’ (‘accrued’ information) repr...
Instantaneous risk of onward transmission of foot-and-mouth disease in Miyazaki 2010 in first 5 weeks and the final week.
(TIF)
Predicted final total culls for weeks 1–12 for several control strategies for the UK 2001 outbreak of foot-and-mouth disease.
A) Predictions of final total culls at the first 12 weeks throughout the 2001 outbreak in UK under seven control strategies (week 1 represents 26 February 2001). Columns denoted ‘Ac’ (‘accrued’ information) represent those s...
Marginal distribution of ϕ2 (exponential term for susceptibility of pigs) versus ζ2 (multiplicative factor for susceptibility of pigs relative to cattle) for the first six weeks of the Miyazaki outbreak.
(TIF)
Algorithm for the calculation of the proportion of times each intervention is chosen as optimal.
(DOCX)
Expected number of undetected infections per county per week in the 2001 UK outbreak, weeks 1–16, as estimated under accrued information (y-axis) and complete information (x-axis).
Those estimated using ‘accrued information’ only used data available at the week in question whereas those estimated under ‘complete information’ were estimated using al...
Marginal posterior predictive distribution of 16 parameters in the epidemic model for the first 11 weeks.
Distributions in red are estimated for the outbreak in Miyazaki blue for parameters the UK. Parameters shown on the log scale are γ1, ε1, and ε2.
(TIF)
Marginal posterior distribution of ψ1 (multiplicative term for contribution to infectious pressure from cattle) versus log γ1 (multiplicative factor contributing the infection pressure from infected farms) for the first 6 weeks of the 2001 UK outbreak.
(TIF)
Expected number of undetected infections per county per week in the 2010 Miyazaki outbreak as estimated under accrued (y-axis) and complete information (x-axis).
Those estimated using ‘accrued information’ only used data available at the week in question whereas those estimated under ‘complete information’ were estimated using all data from the out...
Predicted final total culls for weeks 13–28 for several control strategies for the UK 2001 outbreak of foot-and-mouth disease.
A) Predictions of final total culls at weeks 13–28 throughout the 2001 outbreak in UK under seven control strategies (week 1 represents 26 February 2001). Columns denoted ‘Ac’ (‘accrued’ information) represent those simulat...
Histogram of outbreak sizes ≥ 0.005.
Population densities are simulated from 2000 to 10201 at intervals of 200. Time step τ = 0.1, transmission rate δ = 2, recovery rate ρ = 0.2, vaccine intensity ε = 20, and interaction scale α = 1. For each population density, 60 simulation replicates were run for each vaccination diffusion rate 0.5 < μ < 50 at i...
Overview, Design concepts and Details (ODD) protocol.
(DOCX)